The Portuguese ace was furious when he was shown a second yellow card for going down in the box following a challenge by Samuel Umtiti.
The 32-year-old initially walked away in disbelief with his hands on his head but then turned back towards the official before pushing him with his right hand.
Just two minutes before, Ronaldo had already been booked for taking his shirt off after scoring a screamer to give his side a 2-1 lead in the second half.
And it appears losing his cool could cost him a lengthy ban.
In Article 96 of the Spanish federation’s rule book it is stated that that a “grab, push or shake” on a referee in a manner that is “slightly violent” sees a player banned for four to 12 matches.
In the referee’s match report he stated: “Once I showed him the red card, the player (Ronaldo) pushed me lightly showing discomfort.”
The federation will now decide on the severity of Ronaldo’s actions before determining what ban he should receive.
Cristiano Ronaldo scores, copies Lionel Messi’s celebration, is sent off and PUSHES ref in just two crazy minutes during Real Madrid’s 3-1 Super Cup win at Clasico rivals Barcelona
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It was the only blotch on a fine night at the Nou Camp for Zinedine Zidane’s side.
Gerard Pique put the ball in his own net before Lionel Messi levelled the scores from the penalty spot.
Ronaldo then finished off a fine counter attack before the talented Marco Asensio bagged Real Madrid’s third.
Real host Barca in the second leg on Wednesday but will be without Ronaldo.